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16635 Commits

Author SHA1 Message Date
Axel Kohlmeyer fbc9cf8354
fix huge memory leak 2019-02-28 17:53:17 -05:00
Axel Kohlmeyer c555f7e2ed
update permissions 2019-02-28 17:52:53 -05:00
Axel Kohlmeyer 14e6c126a8
Merge pull request #1314 from charlessievers/OptimizedDynamicalMatrix 
add command to compute the Dynamical Matrix
 2019-02-28 17:08:36 -05:00
Axel Kohlmeyer 50fef541c2
add x-ref 2019-02-28 15:50:59 -05:00
Axel Kohlmeyer 5fd033c0a2
add one more false positive required by recent changes 2019-02-28 15:49:48 -05:00
Axel Kohlmeyer 1d2eab5e1b
update attribution information in Package details documentation 2019-02-28 15:26:36 -05:00
Axel Kohlmeyer 7062bc862e
remove third_order command and ASE based examples to be added in a new pull request 2019-02-28 15:21:48 -05:00
Axel Kohlmeyer 9298fe7868
fix segfault and copy-n-modify issues with third order command 2019-02-28 14:45:42 -05:00
Axel Kohlmeyer 16946d8c6d
integrate dynamical_matrix command into LAMMPS manual 2019-02-28 14:45:07 -05:00
Axel Kohlmeyer 286112ffbc
count each force computation as one simulation step. this avoids accessing uninitialized data, too. 2019-02-28 11:00:55 -05:00
Axel Kohlmeyer 326a97624e
Merge pull request #1317 from ornladios/adios2-master 
USER-ADIOS package with ADIOS 2.x
 2019-02-27 17:24:12 -05:00
Axel Kohlmeyer 80392224cd
Merge pull request #1351 from ellio167/kim-2.0.1 
Bump KIM API version to 2.0.1
 2019-02-27 17:21:30 -05:00
Axel Kohlmeyer b60f0f754c
small tweaks to USER-ADIOS docs 2019-02-27 17:18:08 -05:00
Axel Kohlmeyer 6bd56c2a85
update author attribution 2019-02-27 17:08:13 -05:00
Axel Kohlmeyer a4e580879c
Merge pull request #1347 from akohlmey/collected-small-fixes 
Collected small fixes for the next patch release
 2019-02-27 17:02:21 -05:00
Ryan S. Elliott 54e5c76333 Bump KIM API version to 2.0.1 2019-02-27 15:50:08 -06:00
Axel Kohlmeyer 9cc7bea05d
bugfix for changes in #1340 2019-02-27 16:09:46 -05:00
Axel Kohlmeyer 099b9baf0d
update blob about providing a suitable e-mail contact in PR template 2019-02-27 16:08:42 -05:00
Axel Kohlmeyer 28f1ad9145
update License section to unconditionally confirm GPL and LGPL licensing 2019-02-27 16:08:41 -05:00
Axel Kohlmeyer f178cc0a73
add template for help requests and generic issues 
NOTE: the help request issue template actually asks people
to post to the lammps-users mailing list.
 2019-02-27 16:08:41 -05:00
Axel Kohlmeyer 9185f28a12
correct compute group/group documentation for use with EAM styles 2019-02-27 16:08:41 -05:00
Axel Kohlmeyer 229ded45ee
pull request template update 2019-02-27 16:08:41 -05:00
Axel Kohlmeyer ba320967a5
fix variable delete bug reported in #1346 2019-02-27 16:08:41 -05:00
Axel Kohlmeyer 73401d02c0
convert a couple of inputs from using pair style reax to reax/c 2019-02-27 16:08:41 -05:00
Axel Kohlmeyer eb39866e87
Merge pull request #1340 from akohlmey/bonus-data-checks 
Bonus data checks and updates. Part 1
 2019-02-27 15:10:58 -05:00
Axel Kohlmeyer 0efc3765f8
add warning when writing incomplete data file due to bonus data 2019-02-27 14:57:25 -05:00
Axel Kohlmeyer 05774ed894
Merge pull request #1315 from jan-janssen/patch-1 
Adjust LAMMPS python module for compiling the shared library with CMake, which uses a different extension on MacOS X.
 2019-02-27 14:46:53 -05:00
Axel Kohlmeyer c4d081b507
hide output to stderr when looking for adios-config. we only need the error status. 2019-02-27 14:16:36 -05:00
Axel Kohlmeyer 9bec93faa9
update spell-checking false positives for USER-ADIOS package 2019-02-26 19:51:18 -05:00
Axel Kohlmeyer 9178b9446a
remove trailing whitespace 2019-02-26 19:50:50 -05:00
Axel Kohlmeyer 36b8271e04
Merge pull request #1348 from akohlmey/create-atoms-optimization 
Optimization for create_atoms with regions (2nd attempt)
 2019-02-26 12:19:37 -05:00
Axel Kohlmeyer de29763d1a
new attempt at the create_atoms optimization for small regions in large boxes 
this passes the test input with the rotated lattice
 2019-02-25 17:11:54 -05:00
Axel Kohlmeyer 394fd751d1
Merge pull request #1344 from erozic/bugfix-library-scatter-subset 
Fixed bug in lammps_scatter_atoms_subset...
 2019-02-22 15:10:33 -05:00
Axel Kohlmeyer d76569c033
Merge pull request #1320 from eofetis/manual-pdf-support 
Add support for Sphinx+PDF+MathJax
 2019-02-22 15:10:13 -05:00
Axel Kohlmeyer e6df92e65a
Merge pull request #1011 from ellio167/kim-v2-update 
KIM v2 update
 2019-02-21 20:06:59 -05:00
Axel Kohlmeyer e6a7c8b03b
Merge pull request #1335 from donatas-surblys/langevin-tally-zero 
correct fix langevin with tally yes zero yes
 2019-02-21 20:06:44 -05:00
Eugen Rožić b38033bc59 Fixed bug in lammps_scatter_atoms_subset... 
- ids was ignored for the single-value integer arrays (e.g. type, id, ...)
 2019-02-21 01:07:46 +01:00
Norbert Podhorszki 3ad268739b Add dump adios to PDF build. Update example config with better documentation 2019-02-20 17:02:48 -05:00
Norbert Podhorszki a5f20305d4 Add user-adios to PACKLIB and PACKEXT 2019-02-20 16:28:51 -05:00
Norbert Podhorszki 2de01cef45 Dump atom/adios and dump custom/adios command notifications 2019-02-20 16:21:07 -05:00
Norbert Podhorszki 1179beb543 Makefile build support for USER-ADIOS and build documentation 2019-02-20 14:42:28 -05:00
Norbert Podhorszki 75fe967876 remove fluff about adios in CMakeLists.txt. 2019-02-20 09:02:24 -05:00
Norbert Podhorszki 9c52a37546 PIMPL implementation of USER-ADIOS to hide internal data from style header file 2019-02-20 09:02:24 -05:00
Norbert Podhorszki a4b9542ba9 remove personal runconf file. cleanup ADIOS2 xml config file for example 2019-02-20 09:02:24 -05:00
Norbert Podhorszki 410d79d8b7 Add an example for USER/adios based on the balance example 2019-02-20 09:02:24 -05:00
Norbert Podhorszki 200fed9d4c Fix basic errors in USER-ADIOS code 2019-02-20 09:02:24 -05:00
Norbert Podhorszki 24234d3a0b Fixed cmake build for ADIOS 2.x 2019-02-20 09:02:24 -05:00
Norbert Podhorszki 8db88b1c02 Added initial untested ADIOS 2.x code with cmake building problems 2019-02-20 09:02:24 -05:00
Axel Kohlmeyer 12bec9cbad
Merge pull request #1339 from pmla/ptm-update 
USER-PTM package update
 2019-02-18 19:43:31 +01:00
Axel Kohlmeyer 9207b8814e
Merge pull request #1341 from rbberger/cmake_detect_changes 
Fixes part of issue #1278
 2019-02-18 08:18:47 +01:00